data_4HDQ # _model_server_result.job_id bWXQM0wUr_b0s6PDFJBosw _model_server_result.datetime_utc '2024-11-12 19:33:16' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4hdq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 4HDQ # _exptl.entry_id 4HDQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.56 _cell.angle_gamma 90 _cell.entry_id 4HDQ _cell.length_a 57.31 _cell.length_b 77.41 _cell.length_c 58.57 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HDQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 B OG SER 17 B SER 17 1_555 E MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 B OG1 THR 35 B THR 35 1_555 E MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc3 E MG MG . B MG 200 1_555 F O1B GNP . B GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc4 E MG MG . B MG 200 1_555 F O1G GNP . B GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 E MG MG . B MG 200 1_555 H O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 E MG MG . B MG 200 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 4HDQ _atom_sites.fract_transf_matrix[1][1] 0.017449 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0017 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012918 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017154 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 GOL A 1 801 1 GOL GOL . E 5 MG B 1 200 200 MG MG . F 6 GNP B 1 201 201 GNP GNP . G 7 HOH A 1 901 3 HOH HOH . G 7 HOH A 2 902 4 HOH HOH . G 7 HOH A 3 903 5 HOH HOH . G 7 HOH A 4 904 6 HOH HOH . G 7 HOH A 5 905 8 HOH HOH . G 7 HOH A 6 906 9 HOH HOH . G 7 HOH A 7 907 11 HOH HOH . G 7 HOH A 8 908 12 HOH HOH . G 7 HOH A 9 909 13 HOH HOH . G 7 HOH A 10 910 15 HOH HOH . G 7 HOH A 11 911 16 HOH HOH . G 7 HOH A 12 912 17 HOH HOH . G 7 HOH A 13 913 18 HOH HOH . G 7 HOH A 14 914 19 HOH HOH . G 7 HOH A 15 915 20 HOH HOH . G 7 HOH A 16 916 21 HOH HOH . G 7 HOH A 17 917 22 HOH HOH . G 7 HOH A 18 918 23 HOH HOH . G 7 HOH A 19 919 24 HOH HOH . G 7 HOH A 20 920 26 HOH HOH . G 7 HOH A 21 921 27 HOH HOH . G 7 HOH A 22 922 28 HOH HOH . G 7 HOH A 23 923 29 HOH HOH . G 7 HOH A 24 924 30 HOH HOH . G 7 HOH A 25 925 31 HOH HOH . G 7 HOH A 26 926 32 HOH HOH . G 7 HOH A 27 927 35 HOH HOH . G 7 HOH A 28 928 36 HOH HOH . G 7 HOH A 29 929 38 HOH HOH . G 7 HOH A 30 930 40 HOH HOH . G 7 HOH A 31 931 43 HOH HOH . G 7 HOH A 32 932 44 HOH HOH . G 7 HOH A 33 933 52 HOH HOH . G 7 HOH A 34 934 54 HOH HOH . G 7 HOH A 35 935 56 HOH HOH . G 7 HOH A 36 936 57 HOH HOH . G 7 HOH A 37 937 58 HOH HOH . G 7 HOH A 38 938 60 HOH HOH . G 7 HOH A 39 939 62 HOH HOH . G 7 HOH A 40 940 65 HOH HOH . G 7 HOH A 41 941 66 HOH HOH . G 7 HOH A 42 942 67 HOH HOH . G 7 HOH A 43 943 68 HOH HOH . G 7 HOH A 44 944 70 HOH HOH . G 7 HOH A 45 945 71 HOH HOH . G 7 HOH A 46 946 73 HOH HOH . G 7 HOH A 47 947 74 HOH HOH . G 7 HOH A 48 948 75 HOH HOH . G 7 HOH A 49 949 76 HOH HOH . G 7 HOH A 50 950 77 HOH HOH . G 7 HOH A 51 951 78 HOH HOH . G 7 HOH A 52 952 80 HOH HOH . G 7 HOH A 53 953 81 HOH HOH . G 7 HOH A 54 954 82 HOH HOH . G 7 HOH A 55 955 83 HOH HOH . G 7 HOH A 56 956 85 HOH HOH . G 7 HOH A 57 957 86 HOH HOH . G 7 HOH A 58 958 87 HOH HOH . G 7 HOH A 59 959 88 HOH HOH . G 7 HOH A 60 960 89 HOH HOH . G 7 HOH A 61 961 91 HOH HOH . G 7 HOH A 62 962 94 HOH HOH . G 7 HOH A 63 963 95 HOH HOH . G 7 HOH A 64 964 96 HOH HOH . G 7 HOH A 65 965 97 HOH HOH . G 7 HOH A 66 966 98 HOH HOH . G 7 HOH A 67 967 99 HOH HOH . H 7 HOH B 1 301 1 HOH HOH . H 7 HOH B 2 302 2 HOH HOH . H 7 HOH B 3 303 7 HOH HOH . H 7 HOH B 4 304 10 HOH HOH . H 7 HOH B 5 305 25 HOH HOH . H 7 HOH B 6 306 33 HOH HOH . H 7 HOH B 7 307 34 HOH HOH . H 7 HOH B 8 308 37 HOH HOH . H 7 HOH B 9 309 41 HOH HOH . H 7 HOH B 10 310 42 HOH HOH . H 7 HOH B 11 311 47 HOH HOH . H 7 HOH B 12 312 49 HOH HOH . H 7 HOH B 13 313 50 HOH HOH . H 7 HOH B 14 314 51 HOH HOH . H 7 HOH B 15 315 53 HOH HOH . H 7 HOH B 16 316 59 HOH HOH . H 7 HOH B 17 317 63 HOH HOH . H 7 HOH B 18 318 64 HOH HOH . H 7 HOH B 19 319 69 HOH HOH . H 7 HOH B 20 320 72 HOH HOH . H 7 HOH B 21 321 84 HOH HOH . H 7 HOH B 22 322 90 HOH HOH . H 7 HOH B 23 323 92 HOH HOH . H 7 HOH B 24 324 93 HOH HOH . H 7 HOH B 25 325 100 HOH HOH . I 7 HOH C 1 1401 48 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG GNP . . . F 6 0.481 4.894 28.867 1 40.59 ? PG GNP 201 B 1 HETATM 2 O O1G GNP . . . F 6 1.206 5.884 27.863 1 30.74 ? O1G GNP 201 B 1 HETATM 3 O O2G GNP . . . F 6 -0.68 5.542 29.603 1 35.01 ? O2G GNP 201 B 1 HETATM 4 O O3G GNP . . . F 6 1.672 4.675 29.951 1 39.41 ? O3G GNP 201 B 1 HETATM 5 N N3B GNP . . . F 6 -0.049 3.371 28.243 1 34.96 ? N3B GNP 201 B 1 HETATM 6 P PB GNP . . . F 6 -1.1 3.194 26.86 1 30.8 ? PB GNP 201 B 1 HETATM 7 O O1B GNP . . . F 6 -0.42 4.23 25.863 1 26.68 ? O1B GNP 201 B 1 HETATM 8 O O2B GNP . . . F 6 -2.534 3.41 27.202 1 29.56 ? O2B GNP 201 B 1 HETATM 9 O O3A GNP . . . F 6 -0.889 1.709 26.376 1 26.47 ? O3A GNP 201 B 1 HETATM 10 P PA GNP . . . F 6 0.124 1.28 25.167 1 31.3 ? PA GNP 201 B 1 HETATM 11 O O1A GNP . . . F 6 -0.568 1.685 23.858 1 30.58 ? O1A GNP 201 B 1 HETATM 12 O O2A GNP . . . F 6 1.53 1.683 25.503 1 29.67 ? O2A GNP 201 B 1 HETATM 13 O O5' GNP . . . F 6 -0.12 -0.269 25.162 1 31.94 ? O5' GNP 201 B 1 HETATM 14 C C5' GNP . . . F 6 0.06 -0.986 26.407 1 36.57 ? C5' GNP 201 B 1 HETATM 15 C C4' GNP . . . F 6 0.518 -2.433 26.117 1 33.52 ? C4' GNP 201 B 1 HETATM 16 O O4' GNP . . . F 6 -0.611 -3.146 25.612 1 38.79 ? O4' GNP 201 B 1 HETATM 17 C C3' GNP . . . F 6 1.551 -2.6 24.998 1 35.7 ? C3' GNP 201 B 1 HETATM 18 O O3' GNP . . . F 6 2.375 -3.77 25.148 1 37.34 ? O3' GNP 201 B 1 HETATM 19 C C2' GNP . . . F 6 0.722 -2.844 23.758 1 33.03 ? C2' GNP 201 B 1 HETATM 20 O O2' GNP . . . F 6 1.384 -3.499 22.667 1 30.67 ? O2' GNP 201 B 1 HETATM 21 C C1' GNP . . . F 6 -0.433 -3.659 24.318 1 32.92 ? C1' GNP 201 B 1 HETATM 22 N N9 GNP . . . F 6 -1.649 -3.34 23.537 1 32.85 ? N9 GNP 201 B 1 HETATM 23 C C8 GNP . . . F 6 -2.145 -2.108 23.208 1 28.35 ? C8 GNP 201 B 1 HETATM 24 N N7 GNP . . . F 6 -3.281 -2.17 22.506 1 25.99 ? N7 GNP 201 B 1 HETATM 25 C C5 GNP . . . F 6 -3.502 -3.47 22.332 1 28.95 ? C5 GNP 201 B 1 HETATM 26 C C6 GNP . . . F 6 -4.485 -4.303 21.641 1 29.73 ? C6 GNP 201 B 1 HETATM 27 O O6 GNP . . . F 6 -5.472 -3.839 21.065 1 31.48 ? O6 GNP 201 B 1 HETATM 28 N N1 GNP . . . F 6 -4.315 -5.64 21.72 1 33.53 ? N1 GNP 201 B 1 HETATM 29 C C2 GNP . . . F 6 -3.297 -6.213 22.39 1 32.98 ? C2 GNP 201 B 1 HETATM 30 N N2 GNP . . . F 6 -3.205 -7.561 22.48 1 37.91 ? N2 GNP 201 B 1 HETATM 31 N N3 GNP . . . F 6 -2.352 -5.526 23.022 1 31.26 ? N3 GNP 201 B 1 HETATM 32 C C4 GNP . . . F 6 -2.426 -4.212 23.018 1 31.35 ? C4 GNP 201 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 32 #